TY - JOUR
T1 - Reorganized genomic taxonomy of francisellaceae enables design of robust environmental PCR assays for detection of francisella tularensis
AU - Öhrman, Caroline
AU - Sahl, Jason W.
AU - Sjödin, Andreas
AU - Uneklint, Ingrid
AU - Ballard, Rebecca
AU - Karlsson, Linda
AU - McDonough, Ryelan F.
AU - Sundell, David
AU - Soria, Kathleen
AU - Bäckman, Stina
AU - Chase, Kitty
AU - Brindefalk, Björn
AU - Sozhamannan, Shanmuga
AU - Vallesi, Adriana
AU - Hägglund, Emil
AU - Ramirez-Paredes, Jose Gustavo
AU - Thelaus, Johanna
AU - Colquhoun, Duncan
AU - Myrtennäs, Kerstin
AU - Birdsell, Dawn
AU - Johansson, Anders
AU - Wagner, David M.
AU - Forsman, Mats
N1 - Funding Information:
Data Availability Statement: The data generated in this study are openly available in NCBI project accession PRJNA657836. Public available genome data presented in this study is listed in Supplementary Table S1 Acknowledgments: Shotgun sequencing was performed by the SNP&SEQ Technology Platform in Uppsala. The facility is part of the National Genomics Infrastructure (NGI) Sweden and Science for Life Laboratory. The SNP&SEQ Platform is supported by the Swedish Research Council and the Knut and Alice Wallenberg Foundation.
Funding Information:
This work was supported by the Swedish Civil Contingencies Agency [grant number TA 014-2010-01] and the US Department of Homeland Security?s Science and Technology Directorate [award number HSHQDC-17-C-B0021] pursuant to the agreement between the Kingdom of Sweden and the US government on Cooperation in Science and Technology for Homeland Security Matters.
Funding Information:
Funding: This work was supported by the Swedish Civil Contingencies Agency [grant number TA 014-2010-01] and the US Department of Homeland Security’s Science and Technology Directorate [award number HSHQDC-17-C-B0021] pursuant to the agreement between the Kingdom of Sweden and the US government on Cooperation in Science and Technology for Homeland Security Matters.
Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.
PY - 2021/1
Y1 - 2021/1
N2 - In recent years, an increasing diversity of species has been recognized within the family Francisellaceae. Unfortunately, novel isolates are sometimes misnamed in initial publications or multiple sources propose different nomenclature for genetically highly similar isolates. Thus, unstructured and occasionally incorrect information can lead to confusion in the scientific community. Historically, detection of Francisella tularensis in environmental samples has been challenging due to the considerable and unknown genetic diversity within the family, which can result in false positive results. We have assembled a comprehensive collection of genome sequences representing most known Francisellaceae species/strains and restructured them according to a taxonomy that is based on phylogenetic structure. From this structured dataset, we identified a small number of genomic regions unique to F. tularensis that are putatively suitable for specific detection of this pathogen in environmental samples. We designed and validated specific PCR assays based on these genetic regions that can be used for the detection of F. tularensis in environmental samples, such as water and air filters.
AB - In recent years, an increasing diversity of species has been recognized within the family Francisellaceae. Unfortunately, novel isolates are sometimes misnamed in initial publications or multiple sources propose different nomenclature for genetically highly similar isolates. Thus, unstructured and occasionally incorrect information can lead to confusion in the scientific community. Historically, detection of Francisella tularensis in environmental samples has been challenging due to the considerable and unknown genetic diversity within the family, which can result in false positive results. We have assembled a comprehensive collection of genome sequences representing most known Francisellaceae species/strains and restructured them according to a taxonomy that is based on phylogenetic structure. From this structured dataset, we identified a small number of genomic regions unique to F. tularensis that are putatively suitable for specific detection of this pathogen in environmental samples. We designed and validated specific PCR assays based on these genetic regions that can be used for the detection of F. tularensis in environmental samples, such as water and air filters.
KW - Assay
KW - Francisella taxonomy
KW - Phylogeny
KW - Tularemia
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U2 - 10.3390/microorganisms9010146
DO - 10.3390/microorganisms9010146
M3 - Article
AN - SCOPUS:85099312462
SN - 2076-2607
VL - 9
SP - 1
EP - 21
JO - Microorganisms
JF - Microorganisms
IS - 1
M1 - 146
ER -